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Yorodumi- EMDB-8354: Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8354 | |||||||||
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Title | Cryo-EM structure of Polycystic Kidney Disease protein 2 (PKD2), residues 198-703 | |||||||||
Map data | B-factor sharpened, masked map generated from relion auto-refinement and postprocessing | |||||||||
Sample |
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Function / homology | Function and homology information detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development ...detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / : / metanephric part of ureteric bud development / determination of liver left/right asymmetry / renal tubule morphogenesis / metanephric ascending thin limb development / HLH domain binding / basal cortex / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / renal artery morphogenesis / positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / cilium organization / VxPx cargo-targeting to cilium / detection of mechanical stimulus / regulation of calcium ion import / cation channel complex / calcium-induced calcium release activity / placenta blood vessel development / muscle alpha-actinin binding / voltage-gated monoatomic ion channel activity / cellular response to hydrostatic pressure / outward rectifier potassium channel activity / voltage-gated monoatomic cation channel activity / non-motile cilium / cellular response to fluid shear stress / cellular response to osmotic stress / voltage-gated sodium channel activity / inorganic cation transmembrane transport / transcription regulator inhibitor activity / actinin binding / motile cilium / determination of left/right symmetry / protein heterotetramerization / neural tube development / aorta development / ciliary membrane / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / voltage-gated potassium channel activity / cytoplasmic side of endoplasmic reticulum membrane / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / centrosome duplication / sodium ion transmembrane transport / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / embryonic placenta development / monoatomic cation channel activity / release of sequestered calcium ion into cytosol / cellular response to cAMP / potassium ion transmembrane transport / cellular response to calcium ion / cytoskeletal protein binding / basal plasma membrane / ciliary basal body / liver development / establishment of localization in cell / lumenal side of endoplasmic reticulum membrane / calcium ion transmembrane transport / protein tetramerization / cytoplasmic vesicle membrane / cilium / intracellular calcium ion homeostasis / Wnt signaling pathway / cellular response to reactive oxygen species / phosphoprotein binding / mitotic spindle / calcium ion transport / positive regulation of nitric oxide biosynthetic process / cell-cell junction / lamellipodium / regulation of cell population proliferation / heart development / ATPase binding / positive regulation of cytosolic calcium ion concentration / protein homotetramerization / basolateral plasma membrane / transmembrane transporter binding / regulation of cell cycle / negative regulation of cell population proliferation / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Shen PS / Yang X / DeCaen PG / Liu X / Bulkley D / Clapham DE / Cao E | |||||||||
Citation | Journal: Cell / Year: 2016 Title: The Structure of the Polycystic Kidney Disease Channel PKD2 in Lipid Nanodiscs. Authors: Peter S Shen / Xiaoyong Yang / Paul G DeCaen / Xiaowen Liu / David Bulkley / David E Clapham / Erhu Cao / Abstract: The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM ...The Polycystic Kidney Disease 2 (Pkd2) gene is mutated in autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic disorders. Here, we present the cryo-EM structure of PKD2 in lipid bilayers at 3.0 Å resolution, which establishes PKD2 as a homotetrameric ion channel and provides insight into potential mechanisms for its activation. The PKD2 voltage-sensor domain retains two of four gating charges commonly found in those of voltage-gated ion channels. The PKD2 ion permeation pathway is constricted at the selectivity filter and near the cytoplasmic end of S6, suggesting that two gates regulate ion conduction. The extracellular domain of PKD2, a hotspot for ADPKD pathogenic mutations, contributes to channel assembly and strategically interacts with the transmembrane core, likely serving as a physical substrate for extracellular stimuli to allosterically gate the channel. Finally, our structure establishes the molecular basis for the majority of pathogenic mutations in Pkd2-related ADPKD. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8354.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-8354-v30.xml emd-8354.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8354_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_8354_1.png emd_8354_2.png | 178 KB 244.4 KB | ||
Masks | emd_8354_msk_1.map | 27 MB | Mask map | |
Others | emd_8354_half_map_1.map.gz emd_8354_half_map_2.map.gz | 17.9 MB 17.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8354 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8354 | HTTPS FTP |
-Related structure data
Related structure data | 5t4dMC 8355C 8356C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8354.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | B-factor sharpened, masked map generated from relion auto-refinement and postprocessing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2156 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8354_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: RELION half map 2 (relion refine)
File | emd_8354_half_map_1.map | ||||||||||||
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Annotation | RELION half map 2 (relion_refine) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION half map 1 (relion refine)
File | emd_8354_half_map_2.map | ||||||||||||
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Annotation | RELION half map 1 (relion_refine) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hPKD:198-703
Entire | Name: hPKD:198-703 |
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Components |
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-Supramolecule #1: hPKD:198-703
Supramolecule | Name: hPKD:198-703 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293S GnTI-/- / Recombinant plasmid: pFastbac1 |
-Macromolecule #1: hPKD:198-703, Polycystin-2
Macromolecule | Name: hPKD:198-703, Polycystin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 59.429145 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GAMGSRGLWG TRLMEESSTN REKYLKSVLR ELVTYLLFLI VLCILTYGMM SSNVYYYTRM MSQLFLDTPV SKTEKTNFKT LSSMEDFWK FTEGSLLDGL YWKMQPSNQT EADNRSFIFY ENLLLGVPRI RQLRVRNGSC SIPQDLRDEI KECYDVYSVS S EDRAPFGP ...String: GAMGSRGLWG TRLMEESSTN REKYLKSVLR ELVTYLLFLI VLCILTYGMM SSNVYYYTRM MSQLFLDTPV SKTEKTNFKT LSSMEDFWK FTEGSLLDGL YWKMQPSNQT EADNRSFIFY ENLLLGVPRI RQLRVRNGSC SIPQDLRDEI KECYDVYSVS S EDRAPFGP RNGTAWIYTS EKDLNGSSHW GIIATYSGAG YYLDLSRTRE ETAAQVASLK KNVWLDRGTR ATFIDFSVYN AN INLFCVV RLLVEFPATG GVIPSWQFQP LKLIRYVTTF DFFLAACEII FCFFIFYYVV EEILEIRIHK LHYFRSFWNC LDV VIVVLS VVAIGINIYR TSNVEVLLQF LEDQNTFPNF EHLAYWQIQF NNIAAVTVFF VWIKLFKFIN FNRTMSQLST TMSR CAKDL FGFAIMFFII FLAYAQLAYL VFGTQVDDFS TFQECIFTQF RIILGDINFA EIEEANRVLG PIYFTTFVFF MFFIL LNMF LAIINDTYSE VKSDLAQQKA EMELSD |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 12 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II / Details: blot for 7 seconds, -1 mm offset before plunging. | |||||||||
Details | Single particles embedded in lipid nanodiscs. This sample was monodisperse. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 41132 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 31000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1500 / Average exposure time: 0.2 sec. / Average electron dose: 1.35 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |